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<H1><A HREF=".">Aqua server</A></H1>
<H2><A HREF="./redun_chk.html">
Redundancy check</A></H2>
<BR><BR>

<HR>
Please have a look through the documentation of the <A HREF="../doc/AquaRedun.txt">redundancy
check</A>, <A HREF="../doc/redun_method.txt">method</A> and <A HREF="../doc/redun_output.txt">output</A>
or the article (<A HREF="http://www.nmr.chem.uu.nl/~jurgen/R2D2/description.html">Doreleijers
et al., JMB, 1998</A>) in which it is briefly described.

<P>
<HR><FORM METHOD="POST"
ACTION="CGI_LOC/Aqua/redun_chk.pl" 
ENCTYPE="multipart/form-data">

<P>You need to supply both a restraint and a coordinate file.

<P><B>NOE file:<INPUT 
TYPE="file"
NAME="NOE_FILE" 
VALUE=""
SIZE=50 ></B>

<P>The restraint file should be in the AQUA format described 
<A HREF="http://www.nmr.chem.uu.nl/users/rull/pcheck_dir/nmr_manual/manappb.html">here</A>.
You can use the <A HREF="brsvg.noe">example</A>
restraint file (derived from <A HREF="ftp://pdb.pdb.bnl.gov//nmr_restraints/1brv.mr.Z">PDB
mr file for 1BRV</A>).

<P>Please use this <A HREF="qconvert.html">conversion
server</A> if you are unable to provide the AQUA formatted restraint file.
<BR>Only the NOE upper bound distance information will be used in this
check.
<BR><B>PDB file:<INPUT 
TYPE="file" 
NAME="PDB_FILE" 
VALUE="" 
SIZE=50 ></B>

<P><INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-pdb" CHECKED>PDB&nbsp;<INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-xplor">XPLOR&nbsp;<INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-molmol">MOLMOL

<P>The coordinate file should be in <A HREF="http://www.pdb.bnl.gov/pdb-docs/Format.doc/Contents_Guide_21.html">PDB
format</A>. 
You can use the <A HREF="brsvg.pdb">example</A>
structure (first 2 models of PDB entry <A HREF="http://www.pdb.bnl.gov/pdb-bin/send-pdb?filename=1brv">1BRV</A>
). If you use an XPLOR or MOLMOL type of pdb file you can try selecting
that type.

<P><B>OPTIONS:</B>
<TABLE BORDER CELLSPACING=0 CELLPADDING=10 >
<TR>
<TD>
<DL>
<DT>
Threshold (&lt;=10000 %):</DT>

<DD>
<INPUT TEXT NAME="Threshold" VALUE="5" size=4></DD>

<DT>
Check pseudo atoms:</DT>

<DD>
<INPUT TYPE="radio" NAME="Savpseu"VALUE="false"  CHECKED>yes&nbsp;<INPUT TYPE="radio" NAME="Savpseu"VALUE="true"  	>no</DD>

<DT>
Use target distance as lower bound:</DT>

<DD>
<INPUT TYPE="radio" NAME="Usedist"VALUE="true"  	 >yes&nbsp;<INPUT TYPE="radio" NAME="Usedist"VALUE="false" CHECKED  >no</DD>


<DT> <A HREF="../html/terseness.html">Terseness</A> of the output (0[most verbose] through 9[default]):</DT>

<DD>
<INPUT TEXT NAME="Terseness" VALUE="9" size=2></DD>

</DL>
</TD>

<TD>
<DL>
<DT>
Redundancy on <B>upper bound</B> ONLY:</DT>

<DD>
<INPUT TYPE="radio" NAME="Delredu"VALUE="true"		>yes&nbsp;<INPUT TYPE="radio" NAME="Delredu"VALUE="false" CHECKED >no
<I>Normally both upper and lower bounds (if present) should be redudant
for the restraint to be redundant</I></DD>

<DT>
Redundancy on <B>lower bound</B> ONLY:</DT>

<DD>
<INPUT TYPE="radio" NAME="Delredl"VALUE="true"  	 >yes&nbsp;<INPUT TYPE="radio" NAME="Delredl"VALUE="false" CHECKED  >no&nbsp;</DD>

<DT>
<I>Don't check both options</I>&nbsp;</DT>
</DL>
</TD>
</TR>
</TABLE>
<B>NOTES:</B> A lower bounds &lt;= 1.8 &Aring; is considered as not being
a lowerbound.

<P><INPUT 
TYPE="submit" 
NAME="SUBMIT"
VALUE="Start uploading the Query!"></FORM>
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<P>Contact the 
<A HREF="mailto:jurgenfd@gmail.com">author</A> or 
<A HREF="mailto:WEBMASTER">webmaster</A>
for help, when required.
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